Running

Functions for starting/stopping the phylotaR pipeline.

setup()

Set-up parameters

run()

Run phylotaR pipeline

restart()

Restart a phylotaR pipeline run

reset()

Reset a phylotaR pipeline run

parameters()

Default parameters

parameters_reset()

Change parameters in a working directory

taxise_run()

Run taxise stage

download_run()

Run download stage

clusters_run()

Run the cluster stage

clusters2_run()

Run the cluster2 stage

Tools

Tools for interacting with the Phylota object

read_phylota()

Generate a Phylota object in R

drop_by_rank()

Reduce clusters to specific rank

drop_clstrs()

Drop cluster records from phylota object

drop_sqs()

Drop sequences in a cluster

get_clstr_slot()

Get slot data for each cluster record

get_sq_slot()

Get slot data for each sequence

get_tx_slot()

Get slot data for each taxon record

get_nsqs()

Count number of sequences

get_ntaxa()

Count number of unique taxa

get_txids()

Get taxonomic IDs by rank

is_txid_in_clstr()

Is txid in cluster?

is_txid_in_sq()

Is txid in sequence?

list_clstrrec_slots()

List all ClstrRec slots

list_ncbi_ranks()

List all NCBI Ranks

list_seqrec_slots()

List all SeqRec slots

list_taxrec_slots()

List all TaxRec slots

calc_wrdfrq()

Calculate word frequencies

calc_mad()

Calculate MAD score

write_sqs()

Write out sequences

plot_phylota_treemap()

Plot treemap of Phylota object

plot_phylota_pa()

Plot presence/absence matrix

get_stage_times()

Get run times for different stages

Data

Example Phylota objects

aotus

Example phylota object (aotus)

bromeliads

Example phylota object (bromeliads)

cycads

Example phylota object (cycads)

dragonflies

Example phylota object (dragonflies)

sturgeons

Example phylota object (sturgeons)

tardigrades

Example phylota object (tardigrades)

tinamous

Example phylota object (tinamous)

yeasts

Example phylota object (yeasts)

Classes

S4 classes

as.character(<ClstrArc>) show(<ClstrArc>) print(<ClstrArc>) str(<ClstrArc>) summary(<ClstrArc>) `[[`(<ClstrArc>,<character>) `[`(<ClstrArc>,<character>,<missing>,<missing>)

Cluster record archive

as.character(<ClstrRec>) show(<ClstrRec>) print(<ClstrRec>) str(<ClstrRec>) summary(<ClstrRec>)

Cluster record

as.character(<Phylota>) show(<Phylota>) print(<Phylota>) str(<Phylota>) summary(<Phylota>) `[[`(<Phylota>,<character>)

Phylota object

as.character(<SeqArc>) show(<SeqArc>) print(<SeqArc>) str(<SeqArc>) summary(<SeqArc>) `[[`(<SeqArc>,<character>) `[`(<SeqArc>,<character>,<missing>,<missing>)

Sequence record archive

as.character(<SeqRec>) show(<SeqRec>) print(<SeqRec>) str(<SeqRec>) summary(<SeqRec>)

Sequence record

as.character(<TaxDict>) show(<TaxDict>) print(<TaxDict>) str(<TaxDict>) summary(<TaxDict>)

Taxonomic record dictionary

as.character(<TaxRec>) show(<TaxRec>) print(<TaxRec>) str(<TaxRec>) summary(<TaxRec>)

Taxonomic record

Taxise (private)

Internal functions for running the taxise stage, use phylotaR::: to access.

rank_get()

Get rank

descendants_get()

Get descendants

sqs_count()

Count number of sequences for txid

clade_select()

Get all node IDs that will be processed

txnds_count()

Count number of descending taxonomic nodes

txids_get()

Searches for descendant taxonomic IDs

parent_get()

Get taxonomic parent

tax_download()

Download taxonomic records

taxdict_gen()

Generate taxonomic dictionary

taxtree_gen()

Generate taxonomic tree

Download (private)

Internal functions for running the download stage, use phylotaR::: to access.

searchterm_gen()

Construct GenBank Search Term

seq_download()

Download sequences for txids

seqarc_gen()

Generate sequence archive

seqrec_augment()

Augment sequence records list

seqrec_convert()

Convert raw Entrez gb text record to SeqRecs

seqrec_gen()

Generate sequence record

seqrec_get()

seqrec_get

hierarchic_download()

Hierarchically get sequences for a txid

sids_get()

Return random set of sequence IDs

Cluster (private)

Internal functions for running the cluster stage, use phylotaR::: to access.

blast_clstr()

Cluster BLAST Results

blast_filter()

Filter BLAST results

blast_sqs()

BLAST All vs All

blastdb_gen()

Generate a BLAST database

blastn_run()

Launch blastn

clstr_all()

Hierarchically cluster all sequences of a txid

clstr_direct()

Cluster sequences directly associated with txid

clstr_sqs()

Identify clusters from sequences

clstr_subtree()

Cluster all sequences descending from a txid

clstrarc_gen()

Generate cluster archive container class

clstrarc_join()

Join two cluster archive

clstrrec_gen()

Generate list of clusters

clstrs_calc()

Calculate clusters for all sequences in wd

Cluster2 (private)

Internal functions for running the cluster2 stage, use phylotaR::: to access.

seeds_blast()

BLAST seed sequences

clstr2_calc()

Cluster sets of clusters identified in cluster stage

clstrs_join()

Join clusters for merging

clstrs_merge()

Merge joined clusters

clstrs_renumber()

Renumber cluster IDs

Misc (private)

Miscellaneous internal functions, use phylotaR::: to access.

blast_setup()

Ensures NCBI BLAST tools are installed

download_obj_check()

Check an object returned from rentrez function

safely_connect()

Safely run rentrez function

search_and_cache()

Run rentrez function and cache results

batcher()

Download in batches

info()

Write info message to log

error()

Write error message to log

warn()

Write warning message to log

blastcache_load()

Load BLAST results from cache

blastcache_save()

Save BLAST results to cache

sids_check()

Check if sids exist

sids_load()

Load sids from cache

sids_save()

Save sids to cache

cache_rm()

Delete a cache

cache_setup()

Set-up a cache

sqs_save()

Save sequences to cache

ncbicache_load()

Retrieve cached NCBI query

ncbicache_save()

Save NCBI query result to cache

stages_run()

Sequentially run each stage

stage_args_check()

Check stage arguments

mk_txid_in_sq_mtrx()

Return matrix of txid in sequence

obj_check()

Check if an object exists

obj_load()

Load a named object from the cache

obj_save()

Save a named object in the cache

summary_phylota()

Summarise clusters in Phylota Table

parameters_load()

Load parameters from cache

progress_init()

Initialise progress list in cache

progress_read()

Read the progress from cache

progress_reset()

Reset progress

progress_save()

Save current progress

cmdln()

Run a command via terminal/command prompt

update_phylota()

Update slots

parameters_setup()

Set Up Parameters

clstrs_save()

Save clusters to cache

gb_extract()

Extract elements from a raw GenBank record

rawseqrec_breakdown()

Breakdown a sequence record into its features